Problems encountered frequently during vaccine delivery vector development include poor foreign protein expression, inefficient or incomplete post-translational processing of the immunogen, diminished vector propagation, and gene insert instability. These problems are often related to the foreign gene being nonessential for vector propagation and the negative effect on replicative fitness that often is conferred by the biological or physical characteristics of the nucleotide sequence or the encoded protein.
Earlier ‘gene optimization’ procedures used to develop gene inserts for vaccine vectors focused primarily on designing synthetic coding sequences with the characteristics of highly expressed cellular mRNAs (Andre et al. 1998. J Virol 72:1497-1503, Barouch 2006. The Journal of pathology 208:283-289, Donnelly et al. 1997. DNA vaccines. Annu Rev Immunol 15:617-648 and Haas et al. 1996. Codon usage limitation in the expression of HIV-1 envelope glycoprotein. Current biology: CB 6:315-324). Although this general optimization approach often increases expression of the encoded polypeptide, it also can result in a gene insert that is poorly compatible with the vector because the expressed protein is cytotoxic and/or the engineered nucleotide sequence is difficult to replicate and unstable. Accordingly, there is a need to develop a gene design approach that makes it possible to abundantly express foreign proteins while also reducing the negative effect caused by introducing foreign gene sequences into a vector genetic background.
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